Influenza Viral Genomics and Evolution

流感病毒基因组学和进化

• 批准号: 7732646
• 负责人: Jeffery Taubenberger
• 金额: $ 86.43万
• 依托单位: NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/7732646
• 关键词: Alaska; Alcohol consumption; Animals; Area; Avian Influenza A Virus; Biological Assay; Biology; Birds; Cessation of life; Complex; Data Set; Diagnostic; Domestic Animals; Domestic Fowls; Ducks; Ecology; Environmental Risk Factor; Epidemic; Epidemiology; Equus caballus; Ethanol; Evolution; Exhibits; Family suidae; Genes; Genetic Variation; Genome; Genomics; Goals; Hemagglutinin; Human; Individual; Infection; Influenza; Influenza A Virus, H1N1 Subtype; Influenza A virus; Link; Location; Medical Surveillance; Methods; Minor; Modeling; Molecular; Morbidity - disease rate; Natural Selections; Neuraminidase; Numbers; Pattern; Phylogenetic Analysis; Play; Population; Process; Property; RHOA gene; Rate; Readiness; Recording of previous events; Relative (related person); Reverse Transcriptase Polymerase Chain Reaction; Role; Sampling; Screening procedure; Seasons; Source; Swab; Thinking; Time; United States; Vaccines; Variant; Viral; Viral Genome; Virus; Wing; base; design; falls; fitness; genome sequencing; homologous recombination; influenza epidemic; influenzavirus; lead ion; migration; mortality; novel; pandemic disease; pandemic influenza; pathogen; pressure; success; wild bird

Influenza A viruses (IAV) are significant human pathogens causing yearly epidemics and occasional pandemics. Past pandemics have resulted in significant morbidity and mortality. The 1918 influenza pandemic was thought to have resulted in the death of at least 675,000 people in the U.S., and 40 million people worldwide. Annual influenza A virus epidemics are also very significant, resulting in approximately 30,000 deaths in the U.S. per year. Pandemic strains of influenza emerge periodically and are thought to be derived ultimately from avian influenza A viruses. The natural reservoir of influenza A viruses is thought to be wild waterfowl. Genetically and antigenically diverse influenza A viruses circulate in wild birds and viral strains from this pool can adapt to new hosts, including humans and domestic animals. Influenza A viruses are also significant pathogens for agriculturally important animals like poultry, swine, and horses. Understanding the mechanisms of host switching are very important for surveillance and pandemic preparedness. Understanding the molecular basis underlying the annual evolution of human influenza will aid in vaccine strain selection. Human influenza A virus evolution: Understanding the evolutionary dynamics of human influenza A virus (IAV) is central to its surveillance and control. It was demonstrated that intrasubtypic reassortment is commonly observed in human H1N1 viruses, using a data set of 71 representative complete genome sequences sampled between 1918 and 2006. Specifically, we demonstrated that the severe 1947 epidemic strain acquired novel PB2 and HA genes through intrasubtypic reassortment, which may explain the abrupt antigenic evolution of this virus. Similarly, the severe 1951 influenza epidemic may also have been associated with reassortant H1N1 viruses. Another analysis of human IAV evolution examined the genome-scale evolutionary dynamics of IAV. How genomic processes relate to global influenza epidemiology, in which the H3N2 and H1N1 subtypes co-circulate, is still poorly understood. Through an analysis of 1,302 complete viral genomes sampled from temperate populations in both hemispheres, we showed that the genomic evolution of IAV is characterized by a complex interplay between frequent reassortment and periodic selective sweeps. The H3N2 and H1N1 subtypes exhibit different evolutionary dynamics, with diverse lineages circulating in H1N1, indicative of weaker antigenic drift. These results suggest a source-sink model of viral ecology in which new lineages are seeded from a persistent influenza reservoir source, which we hypothesize to be located in the tropics, to sink populations in temperate regions. These analyses demonstrated that, at any given time, individual IAV gene segments can differ substantially in their relative genetic diversity and hence in phylogenetic history. To determine the causes of these differences in genetic diversity, we estimated the time to the most recent common ancestor (TMRCA) of each segment for each influenza season. Most TMRCAs fall well before the start of the season from which they were sampled, such that multiple lineages persist across multiple epidemic troughs, consistent with our source-sink model. TMRCAs also vary among segments and among years, reflecting the interacting processes of genomic reassortment, natural selection and gene flow. Reassortment places antigenically novel hemagglutinin variants into different genomic backgrounds, a fraction of which may restore, or even increase, the viral replicative fitness that may have been lost as a result of the change in hemagglutinin. In addition to genome-wide interactions, it is essential to consider the complex spatial epidemiological dynamics of influenza if we are to fully understand antigenic evolution. We observed consistent dynamical patterns in two populations illustrative of temperate regions in the Northern and Southern Hemispheres, together with the persistence of viral lineages across multiple epidemics. To resolve these apparently contradictory observations, we proposed the existence of a continuous reservoir or source population, within which the strong selection for antigenic change takes place. Such complexity necessarily means that the long-term success of any individual lineage of influenza virus is dependent not only on its antigenic properties but also on its replicative capacity, its transmissibility and the environmental factors that perhaps underlie the seasonality of influenza in temperate regions. Whether homologous recombination is another mechanism employed in IAV evolution was unclear. To determine the extent of homologous recombination in human influenza A virus, we assembled a data set of 13,852 sequences representing all eight segments and both major circulating subtypes. We concluded that, if it occurs at all, homologous recombination plays only a very minor role in the evolution of human IAV. Avian influenza A virus surveillance: We used ethanol-fixed cloacal swabs to allow avian influenza virus surveillance in remote areas of Alaska. Five hundred paired cloacal samples from dabbling ducks (Northern Pintail, Mallard, Green Wing Teal, and Widgeon) were placed into ethanol and viral transport medium. Additional ethanol-preserved samples were taken. Of the ethanol-preserved samples, 25.6% were AIV RNA-positive by real-time RT-PCR. The hemagglutinin and neuraminidase subtypes were determined for 38 of the first-passage isolates. Five influenza A virus HA-NA combinations were identified: H3N6, H3N8, H4N6, H8N4, and H12N5. In the 500 paired samples, molecular screening detected positive birds at a higher rate than viral isolation. We developed a molecular method for hemagglutinin (HA) subtyping that could be used with fixed samples. We developed a novel method for molecular subtyping of AIV HA genes using degenerate primers designed to amplify all known hemagglutinin subtypes. This method was used to perform subtyping RT-PCR on 191 influenza RNA-positive ethanol-fixed cloacal swabs obtained from 880 wild ducks in central Alaska in 2005. Seven different co-circulating HA subtypes were identified in this study set, including H1, H3, H4, H5, H6, H8, and H12. In addition, 16% of original cloacal samples showed evidence of mixed infection, with samples yielding from two-to-five different HA subtypes. This study further demonstrates the complex ecobiology of avian IAV in wild birds. We determined the complete genomic sequences of 167 wild bird avian IAV isolates from 14 bird species sampled in four locations across the United States representing 29 HA and neuraminidase (NA) subtype combinations, with up to 26% of isolates showing evidence of mixed subtype infection. Through a phylogenetic analysis of the largest data set of avian IAV genomes compiled to date, we observed a remarkably high rate of genome reassortment but little evidence of gene segment association. Evidence for occasional inter-hemisphere gene segment migration and reassortment was obtained. From this, we proposed that avian IAV in wild birds forms transient genome constellations, continually reshuffled by reassortment, in contrast to the spread of a limited number of stable genome constellations that characterizes the evolution of mammalian-adapted IAV.Based on these analyses, we hypothesize that avian IAV in wild birds exists as a large pool of functionally equivalent, and often inter-changeable gene segments that form transient genome constellations, without the strong selective pressure to be maintained as linked genomes.

流感病毒（IAV）是重要的人类病原体，导致年度流行病和偶尔大流行病。过去的大流行病导致了明显的发病率和死亡率。人们认为，1918年的流感大流行导致了美国至少有67.5万人死亡，全世界有4000万人死亡。年度流感病毒流行病也非常重要，每年在美国大约30,000人死亡。流感的大流行菌株定期出现，被认为最终来自禽流感病毒。流感的天然水库被认为是野生水禽。从遗传和抗原上多样化的流感病毒在野生鸟类中循环，该池的病毒菌株可以适应新宿主，包括人类和家畜。流感病毒也是农业重要动物（如家禽，猪和马）的重要病原体。了解宿主切换的机制对于监视和大流行准备非常重要。了解人类流感的年度演变的分子基础将有助于疫苗菌株的选择。 人类流感的一种病毒进化： 了解人类流感病毒（IAV）的进化动力学是其监测和控制的核心。证明在人类H1N1病毒中通常观察到刺内的重新分类，使用了1918年至2006年之间的71个代表性完整基因组序列的数据集。具体，我们具体证明了1947年严重的1947年流行病菌株获得了新的PB2和HAES，通过内部的重新构想，这可以解释这种依从型的依从词，从而解释了这种源头。同样，严重的1951年流感流行病也可能与重新分类的H1N1病毒有关。 对人IAV进化的另一种分析研究了IAV的基因组规模进化动力学。基因组过程与H3N2和H1N1亚型共循环的全球流感流行病学如何相关。通过对两个半球中温带种群采样的1,302个完整病毒基因组的分析，我们表明IAV的基因组演化的特征在于频繁的重新分层和周期性选择性扫描之间存在复杂的相互作用。 H3N2和H1N1亚型表现出不同的进化动力学，在H1N1中循环不同，表明抗原漂移较弱。这些结果表明，病毒生态学的来源 - 链接模型，其中从持续的流感储量来源中播种了新的谱系，我们假设该储量位于热带地区，以沉入温带地区的种群。 这些分析表明，在任何给定的时间，单个IAV基因片段在其相对遗传多样性上可能有很大差异，因此在系统发育史上可能会有很大差异。为了确定遗传多样性差异的原因，我们将每个流感季节的最新祖先（TMRCA）估计为最新的共同祖先（TMRCA）。大多数TMRCA都在抽样的季节开始之前就落下了，因此多个谱系在多个流行病的槽中持续存在，与我们的源链接模型一致。 TMRCA在细分市场和几年中也有所不同，反映了基因组重新分类，自然选择和基因流的相互作用过程。重新分类将抗原新颖的血凝素变体置于不同的基因组背景，其中一部分可能会恢复甚至增加，由于血凝集素的变化而可能丧失的病毒复制适应性。 除了全基因组相互作用外，如果要充分理解抗原性进化，则必须考虑流感的复杂空间流行病学动力学。我们观察到了两个人群中北半球和南半球温带区域的一致动力学模式，以及在多种流行病中的病毒谱系持续存在。为了解决这些明显矛盾的观察，我们提出了连续的储层或源人群的存在，其中发生了强烈的抗原变化选择。这种复杂性必然意味着，流感病毒的任何个体谱系的长期成功不仅取决于其抗原特性，还取决于其复制能力，其可传播性和可能是温带地区流感季节性的环境因素。 同源重组是否是IAV进化中采用的另一种机制尚不清楚。为了确定人类流感病毒中同源重组的程度，我们组装了一个13,852个序列的数据集，该数据集代表所有八个段，均为主要的循环亚型。我们得出的结论是，如果它完全发生，同源重组在人类IAV的进化中仅起着很小的作用。 禽流感病毒监测： 我们使用乙醇固定的泄殖腔拭子允许阿拉斯加偏远地区的禽流感病毒监测。将少量鸭子（北匹尾，野鸭，绿翼蓝绿色和维木）配对的五百个配对的泄殖腔样品放入乙醇和病毒运输培养基中。采集其他保留乙醇的样品。在保留乙醇的样品中，通过实时RT-PCR为AIV RNA阳性25.6％。针对38个第一个小分离株测定了血凝素和神经氨酸酶亚型。鉴定了五种流感病毒HA-NA组合：H3N6，H3N8，H4N6，H8N4和H12N5。在500个配对的样品中，分子筛选以比病毒分离更高的速率检测到阳性鸟类。 我们开发了一种用于血凝素（HA）亚型的分子方法，该方法可与固定样品一起使用。我们使用旨在扩增所有已知的hemagglutin subtypes的简并引物来开发了一种新的AIV HA基因分子亚型的方法。该方法用于对191个流感RNA阳性乙醇固定的胶囊拭子进行亚型RT-PCR，于2005年从阿拉斯加中部的880只野鸭获得。在这项研究集中确定了七个不同的共同循环HA子类型，包括H1，H3，H4，H4，H4，H4，H4，H4，H6，H6，H8，H8和H8和H8和H8和H8和H8和H8，和H8和H12。此外，有16％的原始泄殖腔样品显示出混合感染的证据，样品由两到五种不同的HA亚型产生。这项研究进一步证明了野生鸟类中鸟类IAV的复杂生态学。 我们确定了来自14种在美国四个位置采样的鸟类物种中的167种野生鸟类鸟类IAV分离株的完整基因组序列，代表了29 ha和神经氨酸酶（NA）亚型组合，其中有26％的分离株显示了混合亚型感染的证据。通过对迄今为止汇编的鸟类IAV基因组最大数据集的系统发育分析，我们观察到了基因组的重新分类的高度，但几乎没有基因段关联的证据。获得了偶尔的半球基因段迁移和重新分层的证据。 From this, we proposed that avian IAV in wild birds forms transient genome constellations, continually reshuffled by reassortment, in contrast to the spread of a limited number of stable genome constellations that characterizes the evolution of mammalian-adapted IAV.Based on these analyses, we hypothesize that avian IAV in wild birds exists as a large pool of functionally equivalent, and often inter-changeable gene形成瞬态基因组星座的段，没有强大的选择性压力以保持连接的基因组。

项目成果

The evolutionary genetics and emergence of avian influenza viruses in wild birds.

• DOI: 10.1371/journal.ppat.1000076
• 发表时间: 2008-05-30
• 期刊: PLOS PATHOGENS
• 影响因子: 6.7
• 作者: Dugan, Vivien G.;Chen, Rubing;Spiro, David J.;Sengamalay, Naomi;Zaborsky, Jennifer;Ghedin, Elodie;Nolting, Jacqueline;Swayne, David E.;Runstadler, Jonathan A.;Happ, George M.;Senne, Dennis A.;Wang, Ruixue;Slemons, Richard D.;Holmes, Edward C.;Taubenberger, Jeffery K.
• 通讯作者: Taubenberger, Jeffery K.